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Series GSE180775 Query DataSets for GSE180775
Status Public on Jul 28, 2021
Title Recurrence biomarkers of triple negative breast cancer treated with neoadjuvant chemotherapy combined with anti-EGFR antibodies [Agilent]
Organism Homo sapiens
Experiment type Expression profiling by array
Summary To find metastatic recurrence biomarkers of triple negative breast cancer (TNBC) treated by neoadjuvant chemotherapy and anti-EGFR antibodies (NAT), we evaluated tumor genomic, transcriptomic and immune features, using MSK-IMPACT assay, gene arrays, Nanostring technology and TIL assessment on H&E. Six patients experienced a rapid fatal recurrence (RR) and other 6 had later non-fatal recurrences (LR). Before NAT, RR had low expression of 6 MHC class I and 13 MHC class II genes but were enriched in upregulated genes involved in the cell cycle-related pathways. Their TIL number before NAT in RR was very low (<5%) and did not increase after treatment. In post-NAT residual tumors, RR cases showed high expression of SOX2 and CXCR4. Our results indicate that high expression of cell cycle genes, combined with cold immunological phenotype, may predict strong TNBC resistance to NAT and rapid progression after it. This biomarker combination is worth validation in larger studies.
Overall design Nucleic acids were extracted from frozen tumor tissue (pre-NAT samples) using AllPrep DNA/RNA mini kit (Qiagen France SAS, Courtaboeuf, France) according to the manufacturer’s protocol. RNA quality was verified using the 2100 BioAnalyzer (Agilent Technologies). The extracted material was sent to Helixio (Saint-Beauzire, France), where it was hybridized with gene arrays (Human SurePrint, Agilent Technologies France, Les Ullis, France).
Contributor(s) Scaltriti M, Reis-Filho JS, Radosevic-Robin N, Zhu Y
Citation(s) 34535679
Submission date Jul 25, 2021
Last update date Oct 13, 2021
Contact name Yingjie Zhu
Organization name Memorial Sloan Kettering Cancer Center
Street address 1275 York Avenue
City New York
State/province NY
ZIP/Postal code 10065
Country USA
Platforms (1)
GPL13607 Agilent-028004 SurePrint G3 Human GE 8x60K Microarray (Feature Number version)
Samples (41)
GSM5470636 SAMPLE 1_B87_DR_D
GSM5470637 SAMPLE 2_B52_GE_C
GSM5470638 SAMPLE 3_B72_FAL_SA
BioProject PRJNA749501

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE180775_RAW.tar 510.6 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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